RetrogeneDB ID: retro_sscr_722

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:9544473..9544693(-)
• Located in intron of: ENSSSCG00000007684

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000013936
• Aliases: None
• Description: None

Sequence

>retro_sscr_722
CTGAGGCCTCTGTTTCAGGCAGAGAAGGACCGGAGAATTCTCCAGACGCTTCGGGAGAACTTGGAGGAGGCGGCAATCAT
CCTGAAGGATGTGCCGACAGGAAGGTGGGCGAGTCTGTGTTCCACACAACGCACTGGGTCACCCCAATGATGGGTGAGCT
CTATGGCTGCACACCAATGAGGAGATTCTCAATGCAACCTATGGCTTCATATGGTACACG

Alignment

ORF - retro_sscr_722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.53 %
• Parental protein coverage: 51.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LMPLFQAEKDRRVLQMLRENLEEEAIIMKDVP-DWKVGESVFHTTRWVTPMMGELYG-LRTNEEILSATY
          L.PLFQAEKDRR.LQ.LRENLEE.AII.KDVP.D.KVGESVFHTT.WVTPMMGELYG.L.TNEEIL.ATY
Retrocopy LRPLFQAEKDRRILQTLRENLEEAAIILKDVP<DRKVGESVFHTTHWVTPMMGELYG<LHTNEEILNATY

Parental  GFIWYT
          GFIWYT
Retrocopy GFIWYT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP014902_placenta	0.00 RPM	86.41 RPM
SRP014902_testis	0.71 RPM	62.80 RPM
SRP018288_heart	0.00 RPM	126.04 RPM
SRP018288_kidney	0.00 RPM	82.84 RPM
SRP018288_liver	0.00 RPM	42.38 RPM
SRP018288_lung	0.00 RPM	37.17 RPM
SRP018856_adipose	0.23 RPM	110.90 RPM
SRP035408_brain	0.19 RPM	130.25 RPM
SRP035408_liver	0.00 RPM	87.13 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_722 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_722 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034503	1 retrocopy	retro_cjac_262,
Mus musculus	ENSMUSG00000036199	1 retrocopy	retro_mmus_2453,
Rattus norvegicus	ENSRNOG00000020602	2 retrocopies	retro_rnor_210, retro_rnor_629,
Sorex araneus	ENSSARG00000004735	1 retrocopy	retro_sara_693,
Sus scrofa	ENSSSCG00000013936	3 retrocopies	retro_sscr_707, retro_sscr_722 , retro_sscr_739,
Tursiops truncatus	ENSTTRG00000009880	1 retrocopy	retro_ttru_1141,